sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4mcd | 22L | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4mcd | 22L | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 1.000 | |
| 1uam | SAH | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.582 | |
| 4yvj | SFG | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.550 | |
| 1ual | SAH | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.540 | |
| 4ig6 | SAH | tRNA (guanine-N(1)-)-methyltransferase | / | 0.531 | |
| 1p9p | SAH | tRNA (guanine-N(1)-)-methyltransferase | / | 0.501 | |
| 4yvh | SFG | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.482 | |
| 4yvg | SAM | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.475 | |
| 2z0y | SAM | Ribosomal RNA small subunit methyltransferase E | / | 0.474 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.472 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.466 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.466 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.465 | |
| 2cx8 | SAH | Ribosomal RNA small subunit methyltransferase E | / | 0.463 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.462 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1rbz | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.460 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.458 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.458 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 1uak | SAM | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.455 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.455 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.453 | |
| 4kky | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.453 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.452 | |
| 1u4d | DBQ | Activated CDC42 kinase 1 | / | 0.452 | |
| 3kjm | 245 | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.452 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1hwz | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.451 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.451 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.451 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.450 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.450 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.450 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.450 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.450 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.449 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3wrj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.447 | |
| 2xgo | ZKD | Uncharacterized protein | / | 0.446 | |
| 3mj5 | GRM | Replicase polyprotein 1a | 3.4.22 | 0.446 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4o2b | LOC | Tubulin beta-2B chain | / | 0.446 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4jk3 | NAD | Uncharacterized protein | / | 0.445 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.444 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.444 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.444 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.443 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 2r4u | ADP | Glycogen synthase | 2.4.1.21 | 0.443 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.443 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.443 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.443 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.443 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.443 | |
| 4y95 | 746 | Tyrosine-protein kinase | / | 0.443 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.442 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.442 | |
| 1kvk | ATP | Mevalonate kinase | 2.7.1.36 | 0.441 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.441 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.441 | |
| 4a61 | ANP | Plasmid segregation protein ParM | / | 0.441 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.441 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.441 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1kvu | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 2j3n | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.440 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.440 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.440 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.440 |